Comprehensive Analysis of Energy Minima of the 20 Natural Amino Acids

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• 作者：Yongna Yuan ; Matthew J. L. Mills ; Paul L. A. Popelier ; Frank Jensen
• 刊名：Journal of Physical Chemistry A
• 出版年：2014
• 出版时间：September 11, 2014
• 年：2014
• 卷：118
• 期：36
• 页码：7876-7891
• 全文大小：713K
• ISSN：1520-5215

文摘

Energy minima of the 20 natural amino acids (capped by a peptide bond at both the N and the C termini, CH₃鈥揅(鈺怬)鈥揘(H)鈥?H)C_伪(R)鈥揅(鈺怬)鈥揘(H)鈥揅H₃), were obtained by ab initio geometry optimization. Starting with a large number of minima, quickly generated by MarvinView, geometry optimization at the HF/6-31G(d,p) level of theory reduced the number of minima, followed by further optimization at the B3LYP/apc-1 and MP2/cc-pVDZ levels, which caused some minima to disappear and some stable minima to migrate on the Ramachandran map. There is a relation between the number of minima and the size and the flexibility of the side chain. The energy minima of the 20 amino acids are mainly located in the regions of 尾_L, 纬_L, 未_L, and 伪_L of the Ramachandran map. Multipole moments of atoms occurring in the fragment [鈭扤H鈥揅_伪鈥揅(鈺怬)鈭抅 common to all 20 amino acids were calculated at the three levels of theory mentioned above. The near parallelism in behavior of these moments between levels of theory is beneficial toward estimating moments with the more expensive B3LYP and MP2 methods from data calculated with the cheaper HF method. Finally, we explored the transferability of properties between different amino acids: the bond length and angles of the common fragment [鈭扤H鈥揅_伪(H_伪C_尾)鈥揅鈥?鈺怬)鈭抅 in all amino acids except Gly and Pro. All bond lengths are highly transferable between different amino acids, and the standard deviations are small.